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The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System

Maspero Davide, Damiani Chiara, Antoniotti Marco, Graudenzi Alex, Di Filippo Marzia, Vanoni Marco, Caravagna Giulio, Colombo Riccardo, Ramazzotti Daniele, Pescini Dario

Fundamenta Informaticae

2020

Vol. 171, nr 1-4

279--295

The metabolic processes related to the synthesis of the molecules needed for a new round of cell division underlie the complex behaviour of cell populations in multi-cellular systems, such as tissues and organs, whereas their deregulation can lead to pathological states, such as cancer. Even within genetically homogeneous populations, complex dynamics, such as population oscillations or the emergence of specific metabolic and/or proliferative patterns, may arise, and this aspect is highly amplified in systems characterized by extreme heterogeneity. To investigate the conditions and mechanisms that link metabolic processes to cell population dynamics, we here employ a previously introduced multi-scale model of multi-cellular system, named FBCA (Flux Balance Analysis with Cellular Automata), which couples biomass accumulation, simulated via Flux Balance Analysis of a metabolic network, with the simulation of population and spatial dynamics via Cellular Potts Models. In this work, we investigate the influence that different modes of nutrients diffusion within the system may have on the emerging behaviour of cell populations. In our model, metabolic communication among cells is allowed by letting secreted metabolites to diffuse over the lattice, in addition to diffusion of nutrients from given sources. The inclusion of the diffusion processes in the model proved its effectiveness in characterizing plausible biological scenarios.

Multi-scale numerical analysis of the effect of microstructural features on the mechanical behavior of polycrystalline Ti-6Al-4V alloy

Benmessaoud Fatna, Velay Vincent, Cheikh Mohammed, Vidal Vanessa, Boher Christine, Rézaï-Aria Farhad

Engineering Transactions

2019

Vol. 67, iss. 2

227--242

The present work aims to model the influence of microstructural features of Ti-6Al-4V titanium alloy on its mechanical behavior. A multi-scale approach based on crystal plasticity is considered. The elasto-viscoplastic constitutive equations of Meric-Cailletaud are modified to take into consideration the effect of the grain size by introducing the Hall-Petch relationship at the local scale. This modified model is coupled with finite element calculations under small strain assumption to simulate the monotonic mechanical behavior of Ti-6A-4V at local and global scales. It is shown that the mechanical behavior of Ti-6Al-4V is drastically dependent upon the material features. Strong crystallographic texture can result in the formation of hardened and less hardened areas. Moreover, by increasing the grain size scattering, the heterogeneously deformed areas are multiplied. By decreasing the average grain size, the yield strength increases. It is observed that the effects of grain size, grain size scattering and crystallographic texture are coupled.

Multi-scale modeling of deposition and re-sputtering of NixTi1-x thin film in a magnetron sputtering chamber

Dey A., Aich S., Ghosh S., Mohapatra S. S., Kumar A., Behera A.

Computer Methods in Materials Science

2017

Vol. 17, No. 3

153--165

Deposition and re-sputtering of Ni-Ti thin films by magnetron sputtering was simulated using a multi-scale modeling approach. The sputtering of Ni and Ti targets and the transport of sputtered Ni and Ti atoms through the background gas were simulated using a Monte-Carlo approach, while the deposition of the sputtered atom onto the film surface was analyzed using molecular dynamics. The interaction of Ar+ ions with the deposited film under the influence of substrate bias was also simulated using a Monte-Carlo approach. The distribution of sputtered atoms over the substrate and the fraction of total sputtered atoms from Ni and Ti targets that reached the substrate were calculated for an off centred target which made an angle of 30° with the substrate. The effects of target voltage and gas temperature on the distribution of sputtered atom over substrate were studied with the help of the aforesaid simulations. It was observed that with increasing target voltage, the fraction of sputtered atoms reaching the substrate was increased slightly for a pure Ni target, while it showed very little change for a pure Ti target. With increasing gas temperature, the value for the same decreased initially, but increased beyond a critical temperature. The velocities of incident Ni and Ti atoms on the substrate were calculated and it was found that no intrinsic re-sputtering could take place for a Ni0.5Ti0.5 thin film under the simulated conditions. The fraction of deposited atoms that were re-sputtered by Ar+ ions under varying substrate bias was also calculated and was found to increase substantially with the increase in the magnitude of the substrate bias voltage. Finally, the stability of crystalline and amorphous Ni and Ti were estimated on the basis of fraction of atoms re-sputtered using a classical molecular dynamics approach.

Osadzanie i ponowne rozpylania cienkiej warstwy NixTi|.x w magnetronowej komorze napylającej było symulowane z zastosowaniem modelowania wieloskalowego. Rozpylanie Ni i T oraz transport rozpylanych atomów przez gaz w komorze symulowano metodą Monte Carlo, a osadzanie rozpylanych atomów na powierzchni cienkiej warstwy analizowano za pomocą metody dynamiki molekularnej. Oddziaływanie jonów Ar z osadzoną warstwą z uwzględnieniem wpływu nachylenia podłoża symulowano również metodą Monte Carlo. Rozkład osadzanych atomów na podłożu i ułamek osadzonych atomów Ni i Ti które osiągnęły podłoże dla przesuniętego celu nachylonego pod kątem 30° do podłoża. Na podstawie wykonanych symulacji oceniono wpływ napięcia w komorze i temperatury gazu na rozkład osadzonych atomów. Zaobserwowano, że wraz ze wzrostem napięcia dla celu z czystego Ni wzrasta nieznacznie ułamek rozproszonych atomów, które osiągnęły cel. Ten wpływ jest pomijalny dla czystego Ti. Wraz ze wzrostem temperatury wspomniany ułamek początkowo maleje a następnie powyżej temperatury krytycznej zaczyna wzrastać. Obliczone zostały prędkości atomów Ni i Ti osiągających podłoże i zauważono, że ponowne rozpylanie w warunkach symulacji dla cienkiego filmu Ni0.5Ti0.5 nie jest możliwe. W dalszej kolejności obliczono ułamek osadzonych atomów, które zostały ponownie rozpylone przez jony Ar1 dla różnego nachylenia podłoża. Zaobserwowano, że wzrost wielkości napięcia podłoża znacznie zwiększa ten ułamek. W końcowej części pracy na podstawie oceny ułamka atomów ponownie rozpylonych określono stabilność krystalicznego i amorficznego Ni i Ti wykorzystując do tego celu metodę dynamiki molekularnej.